The problem manifests itself when creating a new virtual server when “Redirect HTTP to HTTPS by default?” is turned on. When trying to issue a certificate from let’s encrypt, it will return an error.
The automatically generated redirect in the virtual server conf appears to be the problem:
RedirectMatch /(?!.well-known)(.*)$ https://google.com/$1
When I change this to:
RedirectMatch /(?!.well-known)(.*)$ https://google.com/.well-known/$1
Everything works properly again, I am running Virtualmin 6.00 GPL, Webmin 1.852, Apache 2.4.27